RetrogeneDB ID: retro_itri_343

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393285.1:12607594..12608261(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DNAJA2
• Ensembl ID: ENSSTOG00000004007
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 2 [Source:HGNC Symbol;Acc:14884]

Sequence

>retro_itri_343
GCAGCAGAGTTAATTAATGAAAAGGACTGCTATAAAAAAACGTGAAGGGAAGAGGTTATTCAAGAATTCAAGATTCTTGA
GGTTTGTGTTGGACAAAAGCATGAAACACAGACAGAGAATGACATTCACTGGGGAAGCAGACCAGGCCTCAGGACTGGAG
CCAGGAGACCTTGTTCGTTTGCTACAGGAGAAAGCACATGAGATGGTCCAGAGAAATTGGAATGAATTTCACATGACATA
TAAGATAGGACTTGCTGAAGTTCTATGTGGGTTTCATTGCCCATTTAAGCATCTTGGTGGATATCAAATTAGGACGAATT
ACCATCCTGGCAATGTAATTGAACCAGGGTGTGTTCATGTCGTTGGAGGTGAAGGAATGCCACAGTATCATAATCCCTTT
GCAAAAGACGATCTTTATATAAAATTGGATGTGCATTTTCCTGAAAACAACTGGATCAACCCAAACCAGCCTTCTAAACT
AGAAGATCTTCTGCCATCTAGACCAGAAGTCACTCACATAATTGGAGAAACAGAGGAGGTAAAGCTTCAGGCATCTCATA
ACACTTGAGGCTCAGGAGGTGGTCAGAGGCGTGAAGCATATAATGATGGCTCTGATGAAGAAGGCAGCAGCAACCATCTT
GGACCTGGAGTACAGGGTGCCCATCAG

Alignment

ORF - retro_itri_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.85 %
• Parental protein coverage: 53.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGEVINEKDRCKKCEGKKVIKEVKILEVHV-DKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVF
          ..E.INEKD..KK.....VI.E.KILEV.V.DK.MKH.QR.TFTGEADQA.G.EPGD.V.LLQEK.HE..
Retrocopy AAELINEKDCYKKT*REEVIQEFKILEVCV>DKSMKHRQRMTFTGEADQASGLEPGDLVRLLQEKAHEMV

Parental  QRDGNDLHMTYKIGLVEALCGFQFTFKHLDGRQIVVKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLY
          QR..N..HMTYKIGL.E.LCGF...FKHL.G.QI...Y.PG.VIEPGCV.VV.GEGMPQY.NPF.K.DLY
Retrocopy QRNWNEFHMTYKIGLAEVLCGFHCPFKHLGGYQIRTNYHPGNVIEPGCVHVVGGEGMPQYHNPFAKDDLY

Parental  IKFDVQFPENNWINPDKLSELEDLLPSRPEVPNVIGETEEVELQEFDSTRGSGGGQRREAYNDSSDEESS
          IK.DV.FPENNWINP...S.LEDLLPSRPEV...IGETEEV.LQ....T.GSGGGQRREAYND.SDEE.S
Retrocopy IKLDVHFPENNWINPNQPSKLEDLLPSRPEVTHIIGETEEVKLQASHNT*GSGGGQRREAYNDGSDEEGS

Parental  SHH-GPGVQCAHQ
          S.H.GPGVQ.AHQ
Retrocopy SNHLGPGVQGAHQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_343 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_343 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013794	1 retrocopy	retro_dnov_40,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Ictidomys tridecemlineatus	ENSSTOG00000004007	1 retrocopy	retro_itri_343 ,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Ictidomys tridecemlineatus	ENSSTOG00000009449	1 retrocopy	retro_itri_1356,